Merge pull request #5 from materialdigital/repo-setup

Repo setup

Author: joergwa

.github/workflows/qc.yml

@@ -0,0 +1,33 @@
+# Basic ODK workflow
+
+name: CI
+
+# Controls when the action will run. 
+on:
+  # Triggers the workflow on push or pull request events but only for the main branch
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "ontology_qc"
+  ontology_qc:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+    container: obolibrary/odkfull:v1.6
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v4
+
+      - name: Run ontology QC checks
+        env:
+          DEFAULT_BRANCH: main
+        run: cd src/ontology && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' test IMP=false PAT=false MIR=false
+

.gitignore

@@ -4,7 +4,7 @@
 .DS_Store
 semantic.cache
 bin/
-.trunk/
+
 *.tmp
 *.tmp.obo
 *.tmp.owl
@@ -72,4 +72,4 @@ src/patterns/all_pattern_terms.txt
 /src/metadata
 docs/odk-workflows/RepositoryFileStructure.md
 /docs/odk-workflows
-/docs/odk-workflows
+/docs/odk-workflows

seed/seed-via-docker.sh

@@ -10,7 +10,7 @@
 # More information: https://github.com/INCATools/ontology-development-kit/
 
 # Fingerprint of the configuration file when this Makefile was last generated
-CONFIG_HASH=                52dcf35a1c66087d45fa1f9b557a4c7676f0414cb7b9e52f01ce31840b85ef32
+CONFIG_HASH=                087da44b84d337c9317d66fad93d3ed78e763162782c83586f3b891e30aaa1ca
 
 
 # ----------------------------------------

seed/tto-project.yaml

@@ -14,9 +14,9 @@ Prefix(terms:=<http://purl.org/dc/terms/>)
 
 
 Ontology(<https://w3id.org/pmd/tto/imports/pmdco_import.owl>
-<https://w3id.org/pmd/tto/releases/2025-11-11/imports/pmdco_import.owl>
+<https://w3id.org/pmd/tto/releases/2025-11-19/imports/pmdco_import.owl>
 Annotation(dc:source <https://w3id.org/pmd/co/3.0.0-alpha4>)
-Annotation(owl:versionInfo "2025-11-11")
+Annotation(owl:versionInfo "2025-11-19")
 
 Declaration(Class(obo:BFO_0000001))
 Declaration(Class(obo:BFO_0000002))
@@ -3563,7 +3563,7 @@ AnnotationAssertion(skos:example co:PMD_0000053 "The process of melting aluminum
 SubClassOf(co:PMD_0000053 co:PMD_0000833)
 SubClassOf(co:PMD_0000053 ObjectIntersectionOf(obo:BFO_0000015 ObjectSomeValuesFrom(obo:OBI_0000293 obo:BFO_0000040) ObjectSomeValuesFrom(obo:OBI_0000299 co:PMD_0020139)))
 
-# Class: co:PMD_0000054 (Heizfunktion)
+# Class: co:PMD_0000054 (heating function)
 
 AnnotationAssertion(rdfs:label co:PMD_0000054 "Heizfunktion"@de)
 AnnotationAssertion(rdfs:label co:PMD_0000054 "heating function"@en)
@@ -3837,7 +3837,7 @@ AnnotationAssertion(skos:definition co:PMD_0000530 "Ein Mechanische Eigenschafte
 AnnotationAssertion(skos:example co:PMD_0000530 "Testing the flexural strength of a plastic beam to ensure it can withstand the required load in an engineering application."@en)
 SubClassOf(co:PMD_0000530 co:PMD_0000849)
 
-# Class: co:PMD_0000531 (Analyseverfahren der Biokompatibilität)
+# Class: co:PMD_0000531 (biocompatibility analyzing process)
 
 AnnotationAssertion(rdfs:label co:PMD_0000531 "Analyseverfahren der Biokompatibilität"@de)
 AnnotationAssertion(rdfs:label co:PMD_0000531 "biocompatibility analyzing process"@en)
@@ -4106,7 +4106,7 @@ AnnotationAssertion(skos:definition co:PMD_0000564 "Eine Unterfunktion der Besch
 AnnotationAssertion(co:PMD_0000060 co:PMD_0000564 "true"^^xsd:boolean)
 SubClassOf(co:PMD_0000564 co:PMD_0000575)
 
-# Class: co:PMD_0000565 (coating by soldering)
+# Class: co:PMD_0000565 (Beschichten Durch Löten)
 
 AnnotationAssertion(rdfs:label co:PMD_0000565 "Beschichten Durch Löten"@de)
 AnnotationAssertion(rdfs:label co:PMD_0000565 "coating by soldering"@en)
@@ -4296,7 +4296,7 @@ AnnotationAssertion(skos:definition co:PMD_0000587 "The crack growth is an evolu
 AnnotationAssertion(co:PMD_0000060 co:PMD_0000587 "true"^^xsd:boolean)
 SubClassOf(co:PMD_0000587 co:PMD_0000635)
 
-# Class: co:PMD_0000588 (Kriechprüfmaschine)
+# Class: co:PMD_0000588 (creep testing machine)
 
 AnnotationAssertion(rdfs:label co:PMD_0000588 "Kriechprüfmaschine"@de)
 AnnotationAssertion(rdfs:label co:PMD_0000588 "creep testing machine"@en)
@@ -4431,7 +4431,7 @@ AnnotationAssertion(co:PMD_0000060 co:PMD_0000604 "true"^^xsd:boolean)
 SubClassOf(co:PMD_0000604 co:PMD_0000621)
 DisjointClasses(co:PMD_0000604 co:PMD_0000620)
 
-# Class: co:PMD_0000605 (differential scanning calorimeter)
+# Class: co:PMD_0000605 (Differential-Scanning-Kalorimeter)
 
 AnnotationAssertion(rdfs:label co:PMD_0000605 "Differential-Scanning-Kalorimeter"@de)
 AnnotationAssertion(rdfs:label co:PMD_0000605 "differential scanning calorimeter"@en)
@@ -4826,7 +4826,7 @@ SubClassOf(co:PMD_0000654 co:PMD_0000002)
 SubClassOf(co:PMD_0000654 ObjectIntersectionOf(co:PMD_0000002 ObjectSomeValuesFrom(ObjectInverseOf(co:PMD_0020005) ObjectIntersectionOf(obo:BFO_0000030 ObjectSomeValuesFrom(obo:RO_0000085 obo:BFO_0000034)))))
 SubClassOf(co:PMD_0000654 ObjectSomeValuesFrom(ObjectInverseOf(co:PMD_0020005) ObjectIntersectionOf(obo:BFO_0000030 ObjectSomeValuesFrom(obo:RO_0000085 obo:BFO_0000034))))
 
-# Class: co:PMD_0000655 (furnace)
+# Class: co:PMD_0000655 (Ofen)
 
 AnnotationAssertion(obo:IAO_0000119 co:PMD_0000655 "“Furnace.” Merriam-Webster.com Dictionary, Merriam-Webster, https://www.merriam-webster.com/dictionary/furnace. Accessed 13 Jan. 2023."@en)
 AnnotationAssertion(rdfs:label co:PMD_0000655 "Ofen"@de)
@@ -5695,7 +5695,7 @@ AnnotationAssertion(skos:definition co:PMD_0000874 "A microscope that uses visib
 AnnotationAssertion(skos:definition co:PMD_0000874 "Ein Mikroskop, das sichtbares Licht und Linsen verwendet, um kleine Objekte oder Details zu vergrößern und zu betrachten."@de)
 SubClassOf(co:PMD_0000874 co:PMD_0000855)
 
-# Class: co:PMD_0000875 (Optische Mikroskopie)
+# Class: co:PMD_0000875 (optical microscopy)
 
 AnnotationAssertion(rdfs:label co:PMD_0000875 "Ein Mikroskopieverfahren, das sichtbares Licht und Linsen verwendet, um eine Probe zu vergrößern und abzubilden, und weit verbreitet zur Untersuchung der Mikrostruktur und Morphologie von Materialien ist."@de)
 AnnotationAssertion(rdfs:label co:PMD_0000875 "Optische Mikroskopie"@de)
@@ -5704,7 +5704,7 @@ AnnotationAssertion(skos:definition co:PMD_0000875 "A Microscopy Process that us
 AnnotationAssertion(skos:example co:PMD_0000875 "An example is Light Microscopy."@en)
 SubClassOf(co:PMD_0000875 co:PMD_0000856)
 
-# Class: co:PMD_0000876 (Optisches Profilometer)
+# Class: co:PMD_0000876 (optical profilometer)
 
 AnnotationAssertion(rdfs:label co:PMD_0000876 "Optisches Profilometer"@de)
 AnnotationAssertion(rdfs:label co:PMD_0000876 "optical profilometer"@en)
@@ -5874,7 +5874,7 @@ AnnotationAssertion(skos:definition co:PMD_0000899 "Ein Herstellungsprozess, der
 AnnotationAssertion(skos:example co:PMD_0000899 "Casting, Sintering"@en)
 SubClassOf(co:PMD_0000899 co:PMD_0000833)
 
-# Class: co:PMD_0000900 (primary shaping by additive manufacturing)
+# Class: co:PMD_0000900 (Urformen Durch Additive Fertigung)
 
 AnnotationAssertion(rdfs:label co:PMD_0000900 "Urformen Durch Additive Fertigung"@de)
 AnnotationAssertion(rdfs:label co:PMD_0000900 "primary shaping by additive manufacturing"@en)
@@ -6332,7 +6332,7 @@ AnnotationAssertion(skos:definition co:PMD_0000961 "The sublimation point is a p
 AnnotationAssertion(co:PMD_0000060 co:PMD_0000961 "true"^^xsd:boolean)
 SubClassOf(co:PMD_0000961 co:PMD_0000882)
 
-# Class: co:PMD_0000962 (supercritical fluid chromatography process)
+# Class: co:PMD_0000962 (Überkritische Fluidchromatographie Verfahren)
 
 AnnotationAssertion(rdfs:label co:PMD_0000962 "supercritical fluid chromatography process"@en)
 AnnotationAssertion(rdfs:label co:PMD_0000962 "Überkritische Fluidchromatographie Verfahren"@de)
@@ -6487,7 +6487,7 @@ AnnotationAssertion(skos:example co:PMD_0000979 "Measuring the thermal conductiv
 AnnotationAssertion(co:PMD_0050117 co:PMD_0000979 "TCMP"@en)
 SubClassOf(co:PMD_0000979 co:PMD_0000982)
 
-# Class: co:PMD_0000980 (Wärmeleitfähigkeitsmessfunktion)
+# Class: co:PMD_0000980 (thermal conductivity measuring function)
 
 AnnotationAssertion(rdfs:label co:PMD_0000980 "Wärmeleitfähigkeitsmessfunktion"@de)
 AnnotationAssertion(rdfs:label co:PMD_0000980 "thermal conductivity measuring function"@en)